ALBERT

Description: This investigation analyzes the effect of vortex wakes on the Lagrangian displacement of particles induced by the passage of an obstacle in a two-dimensional incompressible and inviscid fluid. In addition to the trajectories of individual particles, we also study their drift and the corresponding total drift areas in the Föppl and Kirchhoff potential flow models. Our findings, which are obtained numerically and in some regimes are also supported by asymptotic analysis, are compared to the wakeless potential flow which serves as a reference. We show that in the presence of the Föppl vortex wake, some of the particles follow more complicated trajectories featuring a second loop. The appearance of an additional stagnation point in the Föppl flow is identified as a source of this effect. It is also demonstrated that, while the total drift area increases with the size of the wake for large vortex strengths, it is actually decreased for small circulation values. On the other hand, the Kirchhoff flow model is shown to have an unbounded total drift area. By providing a systematic account of the wake effects on the drift, the results of this study will allow for more accurate modeling of hydrodynamic stirring.

Description: One of the most uncertain parameters in stepped spillway design is the length (from the crest) of boundary layer development. The normal velocity profiles responding to the steps as bed roughness are investigated in the developing non-aerated flow region. A detailed analysis of the logarithmic vertical velocity profiles on stepped spillways is conducted through experimental data to verify the computational code and numerical experiments to expand the data available. To determine development length, the hydraulic roughness and displacement thickness, along with the shear velocity, are needed. This includes determining displacement height d and surface roughness length z0 and the relationship of d and z0 to the step geometry. The results show that the hydraulic roughness height ks is the primary factor on which d and z0 depend. In different step height, step width, discharge and intake Froude number, the relations d/ks = 0.22–0.27, z0/ks = 0.06–0.1 and d/z0 = 2.2–4 result in a good estimate. Using the computational code and numerical experiments, air inception will occur over stepped spillway flow as long as the Bauer-defined boundary layer thickness is between 0.72 and 0.79.

Description: A regional-level and dimensionless analysis for designing a domestic rainwater harvesting system (DRWHS) was developed. To consider various combinations of water demand, storage capacity, effective roof area, and rainfall in DRWHS design, two dimensionless ratios were used, namely, demand fraction and storage fraction, along with a relationship between the two ratios. Firstly, Northern Taiwan was divided into four sub-regions through cluster analysis based on the average annual 10-day rainfall distribution at rainfall stations and administrative districts. Easy-to-use dimensionless curves between demand fraction and storage fraction were obtained for five rainwater supply reliabilities of the DRWHS for the four sub-regions. Based on the dimensionless curves, a nomogram was constructed for designing DRWHSs at a rainwater supply reliability of 95% in the sub-region I. Storage capacities determined from the dimensionless curves showed a close fit with those determined from simulated values, but were larger than the values estimated from the method presented in the Green Building Evaluation Manual in most situations. The methodology developed herein can be used effectively for the preliminary design of a DRWHS and for overcoming the difficulties faced in designing a DRWHS without rainfall data and with incomplete rainfall data.

Description: The slow motion of a circular cylinder in a plane Poiseuille flow in a microchannel is analyzed for a wide range of cylinder radii and positions across the channel. The cylinder translates parallel to the channel walls and rotates about its axis. The Stokes approximation is used and the problem is solved analytically using the Papkovich-Fadle eigenfunction expansion and the least-squares method. The stream function and the pressure distribution of the flow field are obtained as results. The force and moment exerted on the cylinder, and the pressure change far from the cylinder, are calculated and shown as functions of the size and location of the cylinder. The results confirm some reciprocal relations exactly. In particular, the translational and rotational velocities of the drifting cylinder in the existing Poiseuille flow are determined. The induced pressure change, when the cylinder drifts in the Poiseuille flow, is also calculated. Some typical streamline patterns, depending on the size and location of the cylinder, are shown and discussed. When the cylinder translates and/or rotates in the channel blocked at infinity, a series of Moffatt eddies appears far from the cylinder in the channel, as expected.

Description: Interactions between capillary and elastic effects are relevant to a variety of applications from micro- and nano-scale manufacturing to biological systems. In this work, we investigate capillary flows in flexible, millimeter-scale cylindrical elastic tubes. We demonstrate that surface tension can cause sufficiently flexible tubes to collapse and coalesce spontaneously through non-axisymmetric buckling, and develop criteria for the initial deformation and complete collapse of a circular tube. Experimental results for capillary rise and evaporation of a liquid in a flexible tube are presented, and several regimes are seen for the equilibrium state of a flexible tube deforming under capillary pressure. Deformations of the tube walls are measured in different regimes and compared with a shell theory model. Analysis and experimental results show that despite the complex and non-axisymmetric deformed shapes of cylindrical structures, the elastocapillary length used in previous literature for flat plates and sheets can be used to predict the behavior of flexible tubes.

Description: We present laboratory experimental results demonstrating that librational forcing of an ellipsoidal container of water can produce intense motions through the mechanism of a libration driven elliptical instability (LDEI). These libration studies are conducted using an ellipsoidal acrylic container filled with water. A particle image velocimetry method is used to measure the 2D velocity field in the equatorial plane over hundreds libration cycles for a fixed Ekman number, E = 2 × 10 −5 . In doing so, we recover the libration induced base flow and a time averaged zonal flow. Further, we show that LDEI in non-axisymmetric container geometries is capable of driving both intermittent and saturated turbulent motions in the bulk fluid. Additionally, we measure the growth rate and amplitude of the LDEI induced excited flow in a fully ellipsoidal container at more extreme parameters than previously studied [Noir et al. , “Experimental study of libration-driven flows in nonaxisymmetric containers,” Phys. Earth Planet. Inter. 204-205 , 1 (2012); Cébron et al. , Phys. Fluids 24 , 061703, “Libration driven elliptical instability,” (2012)]. Excitation of bulk filling turbulence by librational forcing provides a mechanism for transferring rotational energy into turbulent fluid motion and thus can play an important role in the thermal evolution, interior dynamics, and magneto-hydrodynamics of librating bodies, as appear to be common in solar system settings [e.g., Comstock and Bills, “A solar system survey of forced librations in longitude,” J. Geophys. Res. Planets 108 , 1 (2003)].

Description: We numerically study the displacement flow of two iso-viscous Newtonian fluids in an inclined two-dimensional channel, formed by two parallel plates. The results are complementary to our previous studies on displacement flows in pipes and channels. The heavier displacing fluid moves the lighter displaced fluid in the downward direction. Three dimensionless groups largely describe these flows: the densimetric Froude number ( Fr ), the Reynolds number ( Re ), and the duct inclination (β). As a first order approximation, we are able to classify different flow regimes phenomenologically in a two-dimensional ( Fr ; Re cosβ/ Fr )-plane and provide leading order expressions for the transitions between different regimes. The stabilizing and/or de-stabilizing effects of the imposed mean flow on buoyant exchange flows (zero imposed velocity) are described for a broad range of dimensionless parameters.

Description: Compressible granular materials are involved in many applications, some of them being related to energetic porous media. Gas permeation effects are important during their compaction stage, as well as their eventual chemical decomposition. Also, many situations involve porous media separated from pure fluids through two-phase interfaces. It is thus important to develop theoretical and numerical formulations to deal with granular materials in the presence of both two-phase interfaces and gas permeation effects. Similar topic was addressed for fluid mixtures and interfaces with the Discrete Equations Method (DEM) [R. Abgrall and R. Saurel, “Discrete equations for physical and numerical compressible multiphase mixtures,” J. Comput. Phys. 186 (2), 361-396 (2003)] but it seemed impossible to extend this approach to granular media as intergranular stress [K. K. Kuo, V. Yang, and B. B. Moore, “Intragranular stress, particle-wall friction and speed of sound in granular propellant beds,” J. Ballist. 4 (1), 697-730 (1980)] and associated configuration energy [J. B. Bdzil, R. Menikoff, S. F. Son, A. K. Kapila, and D. S. Stewart, “Two-phase modeling of deflagration-to-detonation transition in granular materials: A critical examination of modeling issues,” Phys. Fluids 11 , 378 (1999)] were present with significant effects. An approach to deal with fluid-porous media interfaces was derived in Saurel et al. [“Modelling dynamic and irreversible powder compaction,” J. Fluid Mech. 664 , 348-396 (2010)] but its validity was restricted to weak velocity disequilibrium only. Thanks to a deeper analysis, the DEM is successfully extended to granular media modelling in the present paper. It results in an enhanced version of the Baer and Nunziato [“A two-phase mixture theory for the deflagration-to-detonation transition (DDT) in reactive granular materials,” Int. J. Multiphase Flow 12 (6), 861-889 (1986)] model as symmetry of the formulation is now preserved. Several computational examples are shown to validate and illustrate method’s capabilities.

Description: We perform a theoretical and numerical study of the Coulomb-driven electroconvection flow of a dielectric liquid between two coaxial cylinders. The specific case, where the inner to outer diameter ratio is 0.5, is analyzed. A strong unipolar injection of ions either from the inner or outer cylinder is considered to introduce free charge carriers into the system. A finite volume method is used to solve all governing equations including Navier-Stokes equations and a simplified set of Maxwell’s equations. The flow is characterized by a subcritical bifurcation in the finite amplitude regime. A linear stability criterion and a nonlinear one that correspond to the onset and stop of the flow motion, respectively, are linked with a hysteresis loop. In addition, we also explore the behavior of the system for higher values of the stability parameter. For inner injection, we observe a transition between the patterns made of 7 and 8 cells, before an oscillatory regime is attained. Such a transition leads to a second finite amplitude stability criterion. A simple modal analysis reveals that the competition of different modes is at the origin of this behavior. The charge density, as well as velocity field distributions is provided to help understand the bifurcation behavior.

Description: In this paper, we report the existence of intervalence charge transfer (IVCT) luminescence in Yb-doped fluorite-type crystals associated with Yb 2+ –Yb 3+ mixed valence pairs. By means of embedded cluster, wave function theory ab initio calculations, we show that the widely studied, very broad band, anomalous emission of Yb 2+ -doped CaF 2 and SrF 2 , usually associated with impurity-trapped excitons, is, rather, an IVCT luminescence associated with Yb 2+ –Yb 3+ mixed valence pairs. The IVCT luminescence is very efficiently excited by a two-photon upconversion mechanism where each photon provokes the same strong 4 f 14 –1 A 1g → 4 f 13 ( 2 F 7/2 )5 de g –1 T 1u absorption in the Yb 2+ part of the pair: the first one, from the pair ground state; the second one, from an excited state of the pair whose Yb 3+ moiety is in the higher 4 f 13 ( 2 F 5/2 ) multiplet. The Yb 2+ –Yb 3+ → Yb 3+ –Yb 2+ IVCT emission consists of an Yb 2+ 5 de g → Yb 3+ 4 f 7/2 charge transfer accompanied by a 4 f 7/2 → 4 f 5/2 deexcitation within the Yb 2+ 4 f 13 subshell: [ 2 F 5/2 5 de g , 2 F 7/2 ] → [ 2 F 7/2 ,4 f 14 ]. The IVCT vertical transition leaves the oxidized and reduced moieties of the pair after electron transfer very far from their equilibrium structures; this explains the unexpectedly large band width of the emission band and its low peak energy, because the large reorganization energies are subtracted from the normal emission. The IVCT energy diagrams resulting from the quantum mechanical calculations explain the different luminescent properties of Yb-doped CaF 2 , SrF 2 , BaF 2 , and SrCl 2 : the presence of IVCT luminescence in Yb-doped CaF 2 and SrF 2 ; its coexistence with regular 5 d -4 f emission in SrF 2 ; its absence in BaF 2 and SrCl 2 ; the quenching of all emissions in BaF 2 ; and the presence of additional 5 d –4 f emissions in SrCl 2 which are absent in SrF 2 . They also allow to interpret and reproduce recent experiments on transient photoluminescence enhancement in Yb 2+ -doped CaF 2 and SrF 2 , the appearance of Yb 2+ 4 f –5 d absorption bands in the excitation spectra of the IR Yb 3+ emission in partly reduced CaF 2 :Yb 3+ samples, and to identify the broadband observed in the excitation spectrum of the so far called anomalous emission of SrF 2 :Yb 2+ as an IVCT absorption, which corresponds to an Yb 2+ 4 f 5/2 → Yb 3+ 4 f 7/2 electron transfer.

Description: A classical limit of quantum dynamics can be defined by compensation of the quantum potential in the time-dependent Schrödinger equation. The quantum potential is a non-local quantity, defined in the trajectory-based form of the Schrödinger equation, due to Madelung, de Broglie, and Bohm, which formally generates the quantum-mechanical features in dynamics. Selective inclusion of the quantum potential for the degrees of freedom deemed “quantum,” defines a hybrid quantum/classical dynamics, appropriate for molecular systems comprised of light and heavy nuclei. The wavefunction is associated with all of the nuclei, and the Ehrenfest, or mean-field, averaging of the force acting on the classical degrees of freedom, typical of the mixed quantum/classical methods, is avoided. The hybrid approach is used to examine evolution of light/heavy systems in the harmonic and double-well potentials, using conventional grid-based and approximate quantum-trajectory time propagation. The approximate quantum force is defined on spatial domains, which removes unphysical coupling of the wavefunction fragments corresponding to distinct classical channels or configurations. The quantum potential, associated with the quantum particle, generates forces acting on both quantum and classical particles to describe the backreaction.

Description: Excited states and the ground state of the diatomic molecule RbSr were calculated by post Hartree-Fock molecular orbital theory up to 22 000 cm −1 . We applied a multireference configuration interaction calculation based on multiconfigurational self-consistent field wave functions. Both methods made use of effective core potentials and core polarization potentials. Potential energy curves, transition dipole moments, and permanent electric dipole moments were determined for RbSr and could be compared with other recent calculations. We found a good agreement with experimental spectra, which have been obtained recently by helium nanodroplet isolation spectroscopy. For the lowest two asymptotes (Rb (5 s 2 S) + Sr (5 s 4 d 3 P°) and Rb (5 p 2 P°) + Sr (5 s 2 1 S)), which exhibit a significant spin-orbit coupling, we included relativistic effects by two approaches, one applying the Breit-Pauli Hamiltonian to the multireference configuration interaction wave functions, the other combining a spin-orbit Hamiltonian and multireference configuration interaction potential energy curves. Using the results for the relativistic potential energy curves that correspond to the Rb (5 s 2 S) + Sr (5 s 4 d 3 P°) asymptote, we have simulated dispersed fluorescence spectra as they were recently measured in our lab. The comparison with experimental data allows to benchmark both methods and demonstrate that spin-orbit coupling has to be included for the lowest states of RbSr.

Description: Ozonolysis of alkenes, a principle non-photolytic source of atmospheric OH radicals, proceeds through unimolecular decay of energized carbonyl oxide intermediates, known as Criegee intermediates. In this work, cold dimethyl-substituted Criegee intermediates are vibrationally activated in the CH stretch overtone region to drive the 1,4 hydrogen transfer reaction that leads to OH radical products. IR excitation of (CH 3 ) 2 COO reveals the vibrational states with sufficient oscillator strength, coupling to the reaction coordinate, and energy to surmount the effective barrier (≤ 16.0 kcal mol −1 ) to reaction. Insight on the dissociation dynamics is gleaned from homogeneous broadening of the spectral features, indicative of rapid intramolecular vibrational energy redistribution and/or reaction, as well as the quantum state distribution of the OH X 2 Π (v = 0) products. The experimental results are compared with complementary electronic structure calculations, which provide the IR absorption spectrum and geometric changes along the intrinsic reaction coordinate. Additional theoretical analysis reveals the vibrational modes and couplings that permit (CH 3 ) 2 COO to access to the transition state region for reaction. The experimental and theoretical results are compared with an analogous recent study of the IR activation of syn -CH 3 CHOO and its unimolecular decay to OH products [F. Liu, J. M. Beames, A. S. Petit, A. B. McCoy, and M. I. Lester, Science345, 1596 (2014)].

Description: In the present work, the structural and dynamic properties of liquid and undercooled boron are investigated by means of ab initio molecular dynamics simulation. Our results show that both liquid and undercooled states present a well pronounced short-range order (SRO) mainly due to the formation of inverted umbrella structural units. Moreover, we observe the development of a medium-range order (MRO) in the undercooling regime related to the increase of inverted umbrella structural units and of their interconnection as the temperature decreases. We also evidence that this MRO leads to a partial crystallization in the β-rhombohedral crystal below T = 1900 K. Finally, we discuss the role played by the SRO and MRO in the nearly Arrhenius evolution of the diffusion and the non-Arrhenius temperature dependence of the shear viscosity, in agreement with the experiment.

Description: The properties of dipolar cubic lattices are studied and the paradox of how to obtain a long range polarization in such lattices is resolved by choosing a proper shape of the total system. It has been shown that large but finite number of aligned dipoles prefer to exist as needle shaped macroscopic particles [M. Yoon and D. Tománek, J. Phys.: Condens. Matter22, 455105 (2010)]. The total energy for a particle in such a system has one short range contribution depending on the packing (the chosen lattice) and one long range term depending on the dipole density of the system. We show that the latter term corresponds exactly to the polarization term from a dielectric medium embedding a sphere of the considered system. There is no need to include a dielectric medium in this modeling and the “dielectric stabilization” is generated solely by the dipoles of the system.

Description: A practical hyperdynamics method is proposed to accelerate systems with highly endothermic and exothermic reactions such as hydrocarbon pyrolysis and oxidation reactions. In this method, referred to as the “adaptive hyperdynamics (AHD) method,” the bias potential parameters are adaptively updated according to the change in potential energy. The approach is intensively examined for JP-10 (exo-tetrahydrodicyclopentadiene) pyrolysis simulations using the ReaxFF reactive force field. Valid boost parameter ranges are clarified as a result. It is shown that AHD can be used to model pyrolysis at temperatures as low as 1000 K while achieving a boost factor of around 10 5 .

Description: E -crotonic acid was isolated in cryogenic solid N 2 and xenon matrices, and subjected to Laser ultraviolet (UV) and near-infrared (NIR) irradiations. In the deposited matrices, the two low-energy cis C–O E -cc and E -ct conformers, which are the only forms significantly populated in the gas phase, were observed. UV irradiation (λ= 250 nm) of the compound in N 2 matrix allows for experimental detection, not just of the two low-energy cis C–O isomers of Z -crotonic acid previously observed in the experiments carried out in argon matrix [ Z -cc and Z -ct; R. Fausto, A. Kulbida, and O. Schrems, J. Chem. Soc., Faraday Trans.91, 3755–3770 (1995)] but also of the never observed before high-energy forms of both E - and Z -crotonic acids bearing the carboxylic acid group in the trans arrangement ( E -tc and Z -tc conformers). In turn, NIR irradiation experiments in the N 2 matrix allow to produce the high-energy E -tc trans C–O conformer in a selective way, from the initially deposited E -cc form. The vibrational signatures of all the 6 rotameric structures of the crotonic acids experimentally observed, including those of the new trans C–O forms, were determined and the individual spectra fully assigned, also with support of theoretically obtained data. On the other hand, as found before for the compound isolated in argon matrix, the experiments performed in xenon matrix failed to experimental detection of the trans C–O forms. This demonstrates that in noble gas matrices these forms are not stable long enough to allow for their observation by steady state spectroscopy techniques. In these matrices, the trans C–O forms convert spontaneously into their cis C–O counterparts, by tunnelling. Some mechanistic details of the studied processes were extracted and discussed.

Description: We describe a novel approach for the calculation of local electric dipole moments for periodic systems. Since the position operator is ill-defined in periodic systems, maximally localized Wannier functions based on the Berry-phase approach are usually employed for the evaluation of local contributions to the total electric dipole moment of the system. We propose an alternative approach: within a subsystem-density functional theory based embedding scheme, subset electric dipole moments are derived without any additional localization procedure, both for hybrid and non-hybrid exchange–correlation functionals. This opens the way to a computationally efficient evaluation of local electric dipole moments in (molecular) periodic systems as well as their rigorous splitting into atomic electric dipole moments. As examples, Infrared spectra of liquid ethylene carbonate and dimethyl carbonate are presented, which are commonly employed as solvents in Lithium ion batteries.

Description: The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here, we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding – a central concept to our understanding of the physical chemistry of water, biological systems, and many technologically important materials. Since the hydrogen bond is a somewhat fuzzy entity that covers a broad range of energies and distances, many different criteria have been proposed and used over the years, based either on sophisticate electronic structure calculations followed by an energy decomposition analysis, or on somewhat arbitrary choices of a range of structural parameters that is deemed to correspond to a hydrogen-bonded configuration. We introduce here a definition that is univocal, unbiased, and adaptive, based on our machine-learning analysis of an atomistic simulation. The strategy we propose could be easily adapted to similar scenarios, where one has to recognize or classify structural patterns in a material or chemical compound.

Description: We investigate the performance of Stieltjes Imaging applied to Lanczos pseudo-spectra generated at the coupled cluster singles and doubles, coupled cluster singles and approximate iterative doubles and coupled cluster singles levels of theory in modeling the photodetachment cross sections of the closed shell anions H − , Li − , Na − , F − , Cl − , and OH − . The accurate description of double excitations is found to play a much more important role than in the case of photoionization of neutral species.

Description: For conical intersections of two states ( I,J = I + 1) the vectors defining the branching or g-h plane, the energy difference gradient vector g I,J , and the interstate coupling vector h I,J , can be made orthogonal by a one parameter rotation of the degenerate electronic eigenstates. The representation obtained from this rotation is used to construct the parameters that describe the vicinity of the conical intersection seam, the conical parameters, s I,J x ( R ), s I,J y ( R ), g I,J ( R ), and h I,J ( R ). As a result of the orthogonalization these parameters can be made continuous functions of R , the internuclear coordinates. In this work we generalize this notion to construct continuous parametrizations of conical intersection seams of three or more states. The generalization derives from a recently introduced procedure for using non-degenerate electronic states to construct coupled diabatic states that represent adiabatic states coupled by conical intersections. The procedure is illustrated using the seam of conical intersections of three states in parazolyl as an example.

Description: State averaged complete active space self-consistent field (SA-CASSCF) is a workhorse for determining the excited-state electronic structure of molecules, particularly for states with multireference character; however, the method suffers from known issues that have prevented its wider adoption. One issue is the presence of discontinuities in potential energy surfaces when a state that is not included in the state averaging crosses with one that is. In this communication I introduce a new dynamical weight with spline (DWS) scheme that mimics SA-CASSCF while removing energy discontinuities due to unweighted state crossings. In addition, analytical gradients for DWS-CASSCF (and other dynamically weighted schemes) are derived for the first time, enabling energy-conserving excited-state ab initio molecular dynamics in instances where SA-CASSCF fails.

Description: Modern materials processing applications and technologies often occur far from equilibrium. To this end, the processing of complex materials such as polymer melts and nanocomposites generally occurs under strong deformations and flows, conditions under which equilibrium thermodynamics does not apply. As a result, the ability to determine the nonequilibrium thermodynamic properties of polymeric materials from measurable quantities such as heat and work is a major challenge in the field. Here, we use work relations to show that nonequilibrium thermodynamic quantities such as free energy and entropy can be determined for dilute polymer solutions in flow. In this way, we determine the thermodynamic properties of DNA molecules in strong flows using a combination of simulations, kinetic theory, and single molecule experiments. We show that it is possible to calculate polymer relaxation timescales purely from polymer stretching dynamics in flow. We further observe a thermodynamic equivalence between nonequilibrium and equilibrium steady-states for polymeric systems. In this way, our results provide an improved understanding of the energetics of flowing polymer solutions.

Description: Cohesive interactions between filamentous molecules have broad implications for a range of biological and synthetic materials. While long-standing theoretical approaches have addressed the problem of inter-filament forces from the limit of infinitely rigid rods, the ability of flexible filaments to deform intra-filament shape in response to changes in inter-filament geometry has a profound affect on the nature of cohesive interactions. In this paper, we study two theoretical models of inter-filament cohesion in the opposite limit, in which filaments are sufficiently flexible to maintain cohesive contact along their contours, and address, in particular, the role played by helical-interfilament geometry in defining interactions. Specifically, we study models of featureless, tubular filaments interacting via: (1) pair-wise Lennard-Jones (LJ) interactions between surface elements and (2) depletion-induced filament binding stabilized by electrostatic surface repulsion. Analysis of these models reveals a universal preference for cohesive filament interactions for non-zero helical skew, and further, that in the asymptotic limit of vanishing interaction range relative to filament diameter, the skew-dependence of cohesion approaches a geometrically defined limit described purely by the close-packing geometry of twisted tubular filaments. We further analyze non-universal features of the skew-dependence of cohesion at small-twist for both potentials, and argue that in the LJ model the pair-wise surface attraction generically destabilizes parallel filaments, while in the second model, pair-wise electrostatic repulsion in combination with non-pairwise additivity of depletion leads to a meta-stable parallel state.

Description: The effect of strong intermolecular hydrogen bonding on torsional degrees of freedom is investigated by far-infrared absorption spectroscopy for different methanol dimer isotopologues isolated in supersonic jet expansions or embedded in inert neon matrices at low temperatures. For the vacuum-isolated and Ne-embedded methanol dimer, the hydrogen bond OH librational mode of the donor subunit is finally observed at ∼560 cm −1 , blue-shifted by more than 300 cm −1 relative to the OH torsional fundamental of the free methanol monomer. The OH torsional mode of the acceptor embedded in neon is observed at ∼286 cm −1 . The experimental findings are held against harmonic predictions from local coupled-cluster methods with single and double excitations and a perturbative treatment of triple excitations [LCCSD(T)] and anharmonic. VPT2 corrections at canonical MP2 and density functional theory (DFT) levels in order to quantify the contribution of vibrational anharmonicity for this important class of intermolecular hydrogen bond vibrational motion.

Description: Extensive numerical solutions of the hypernetted-chain (HNC) and Rogers-Young (RY) integral equations are presented for the pair structure of a system of two coupled replicae (1 and 2) of a “soft-sphere” fluid of atoms interacting via an inverse-12 pair potential. In the limit of vanishing inter-replica coupling ɛ 12 , both integral equations predict the existence of three branches of solutions: (1) A high temperature liquid branch ( L ), which extends to a supercooled regime upon cooling when the two replicae are kept at ɛ 12 = 0 throughout; upon separating the configurational and vibrational contributions to the free energy and entropy of the L branch, the Kauzmann temperature is located where the configurational entropy vanishes. (2) Starting with an initial finite coupling ɛ 12 , two “glass” branches G 1 and G 2 are found below some critical temperature, which are characterized by a strong remnant spatial inter-replica correlation upon taking the limit ɛ 12 → 0. Branch G 2 is characterized by an increasing overlap order parameter upon cooling, and may hence be identified with the hypothetical “ideal glass” phase. Branch G 1 exhibits the opposite trend of increasing order parameter upon heating; its free energy lies consistently below that of the L branch and above that of the G 2 branch. The free energies of the L and G 2 branches are found to intersect at an alleged “random first-order transition” (RFOT) characterized by weak discontinuities of the volume and entropy. The Kauzmann and RFOT temperatures predicted by RY differ significantly from their HNC counterparts.

Description: We present a continuum solvent model (CSM) with a smooth cavity for the application in grid-based electronic structure methods. The cavity is identified with the inherently smooth distribution function of a binary mixture at infinite dilution. We obtain a cavity model based on atomic van der Waals radii and one free parameter controlling the overall size. This single parameter is sufficient to adequately reproduce experimental partial molar volumes. The CSM based on this cavity is of similar accuracy in the prediction of aqueous solvation Gibbs energies of small neutral molecules and ions as other CSMs with a smooth cavity. We apply the model to systems in non-aqueous solution, i.e., spiropyran/merocyanin energetics, a proton transfer reaction in dimethyl sulfoxide, and the electrostatic screening of charged gold clusters in an ionic liquid.

Description: Phytoplankton patchiness, namely the heterogeneous distribution of microalgae over multiple spatial scales, dramatically impacts marine ecology. A spectacular example of such heterogeneity occurs in thin phytoplankton layers (TPLs), where large numbers of photosynthetic microorganisms are found within a small depth interval. Some species of motile phytoplankton can form TPLs by gyrotactic trapping due to the interplay of their particular swimming style (directed motion biased against gravity) and the transport by a flow with shear along the direction of gravity. Here we consider gyrotactic swimmers in numerical simulations of the Kolmogorov shear flow, both in laminar and turbulent regimes. In the laminar case, we show that the swimmer motion is integrable and the formation of TPLs can be fully characterized by means of dynamical systems tools. We then study the effects of rotational Brownian motion or turbulent fluctuations (appearing when the Reynolds number is large enough) on TPLs. In both cases, we show that TPLs become transient, and we characterize their persistence.

Description: The model of gas bubble growth in high-viscous gas-saturated magmatic melt, subjected to rapid decompression, is presented in the current study. It is shown that consideration of unsteady character of the process is extremely important in a wide range of supersaturation. The analytical solution is found for the profile of dissolved gas concentration and the rate of bubble growth. The model of kinetics of overall degassing is developed. This model is based on distinguishing the so-called “forbidden” zone in the melt volume with suppressed formation of the new nucleation sites. The simple analytical dependences of the number of nucleating bubbles and typical nucleation time on the value of initial decompression were derived together with time dependence of volumetric concentration of the gas phase. Our results match the available experimental data.

Description: We investigate the effect of viscosity contrast on the stability of gravitationally unstable, diffusive layers in porous media. Our analysis helps evaluate experimental observations of various diffusive (boundary) layer models that are commonly used to study the sequestration of CO 2 in brine aquifers. We evaluate the effect of viscosity contrast for two basic models that are characterized with respect to whether or not the interface between CO 2 and brine is allowed to move. We find that diffusive layers are in general more unstable when viscosity decreases with depth within the layer compared to when viscosity increases with depth. This behavior is in contrast to the one associated with the classical displacement problem of gravitationally unstable diffusive layers that are subject to mean flow. For the classical problem, a greater instability is associated with the displacement of a more viscous, lighter fluid along the direction of gravity by a less viscous, heavier fluid. We show that the contrasting behavior highlighted in this study is a special case of the classical displacement problem that depends on the relative strength of the displacement and buoyancy velocities. We demonstrate the existence of a critical viscosity ratio that determines whether the flow is buoyancy dominated or displacement dominated. We explain the new behaviors in terms of the interaction of vorticity components related to gravitational and viscous effects.

Description: We study the distribution of multivalent counterions next to a dielectric slab, bearing a quenched, random distribution of charges on one of its solution interfaces, with a given mean and variance, both in the absence and in the presence of a bathing monovalent salt solution. We use the previously derived approach based on the dressed multivalent-ion theory that combines aspects of the strong and weak coupling of multivalent and monovalent ions in a single framework. The presence of quenched charge disorder on the charged surface of the dielectric slab is shown to substantially increase the density of multivalent counterions in its vicinity. In the counterion-only model (with no monovalent salt ions), the surface disorder generates an additional logarithmic attraction potential and thus an algebraically singular counterion density profile at the surface. This behavior persists also in the presence of a monovalent salt bath and results in significant violation of the contact-value theorem, reflecting the anti-fragility effects of the disorder that drive the system towards a more “ordered” state. In the presence of an interfacial dielectric discontinuity, depleting the counterion layer at the surface, the charge disorder still generates a much enhanced counterion density further away from the surface. Likewise, the charge inversion and/or overcharging of the surface occur more strongly and at smaller bulk concentrations of multivalent counterions when the surface carries quenched charge disorder. Overall, the presence of quenched surface charge disorder leads to sizable effects in the distribution of multivalent counterions in a wide range of realistic parameters and typically within a distance of a few nanometers from the charged surface.

Description: The reaction free energy for dehydrogenation of phenol, aniline, thiophenol, benzoic acid, and 1,4-benzenediol on the close packed copper, silver, and gold surfaces has been studied by density functional theory calculations. Dehydrogenation of thiophenol is found to be favourable on all three surfaces while aniline does not dehydrogenate on any of them. For phenol, benzenediol and benzoic acid dehydrogenation is favourable on copper and silver only, following the general trend of an increasing reaction free energy when going form gold to silver to copper. This trend can be correlated with the changes in bond lengths within the molecule upon dehydrogenation. While copper is able to replace hydrogen, leaving small changes in the bond lengths of the aromatic ring, the metal-molecule bond is weaker for silver and gold, resulting in a partial loss of aromaticity. This difference in bond strength leads to pronounced differences in adsorption geometries upon multiple dehydrogenations.

Description: Confinement can modify the dynamics, the thermodynamics, and the structural properties of liquid water, the prototypical anomalous liquid. By considering a generic model for anomalous liquids, suitable for describing solutions of globular proteins, colloids, or liquid metals, we study by molecular dynamics simulations the effect that an attractive wall with structure and a repulsive wall without structure have on the phases, the crystal nucleation, and the dynamics of the fluid. We find that at low temperatures the large density of the attractive wall induces a high-density, high-energy structure in the first layer (“templating” effect). In turn, the first layer induces a “molding” effect on the second layer determining a structure with reduced energy and density, closer to the average density of the system. This low-density, low-energy structure propagates further through the layers by templating effect and can involve all the existing layers at the lowest temperatures investigated. Therefore, although the high-density, high-energy structure does not self-reproduce further than the first layer, the structured wall can have a long-range influence thanks to a sequence of templating, molding, and templating effects through the layers. We find that the walls also have an influence on the dynamics of the liquid, with a stronger effect near the attractive wall. In particular, we observe that the dynamics is largely heterogeneous (i) among the layers, as a consequence of the sequence of structures caused by the walls presence, and (ii) within the same layer, due to superdiffusive liquid veins within a frozen matrix of particles near the walls at low temperature and high density. Hence, the partial freezing of the first layer does not correspond necessarily to an effective reduction of the channel's section in terms of transport properties, as suggested by other authors.

Description: We propose a novel quantum chemical method, called the harmonic solvation model (HSM), for calculating thermochemical parameters in the condensed phase, particularly in the liquid phase. The HSM represents translational and rotational motions of a solute as vibrations interacting with a cavity wall of solvent molecules. As examples, the HSM and the ideal-gas model (IGM) were used for the standard formation reaction of liquid water, combustion reactions of liquid formic acid, methanol, and ethanol, vapor–liquid equilibration of water and ethanol, and dissolution of gaseous CO 2 in water. The numerical results confirmed the reliability and applicability of the HSM. In particular, the temperature dependence of the Gibbs energy of liquid molecules was accurately reproduced by the HSM; for example, the boiling point of water was reasonably determined using the HSM, whereas the conventional IGM treatment failed to obtain a crossing of the two Gibbs energy curves for gaseous and liquid water.

Description: In this paper, we examine the behaviour of basic autocatalytic feedback modules involving a species catalyzing its own production, either directly or indirectly. We first perform a systematic study of the autocatalytic feedback module in isolation, examining the effect of different factors, showing how this module is capable of exhibiting monostable threshold and bistable switch-like behaviour. We then study the behaviour of this module embedded in different kinds of basic networks including (essentially) irreversible cycles, open and closed reversible chains, and networks with additional feedback. We study the behaviour of the networks deterministically and also stochastically, using simulations, analytical work, and bifurcation analysis. We find that (i) there are significant differences between the behaviour of this module in isolation and in a network: thresholds may be altered or destroyed and bistability may be destroyed or even induced, even when the ambient network is simple. The global characteristics and topology of this network and the position of the module in the ambient network can play important and unexpected roles. (ii) There can be important differences between the deterministic and stochastic dynamics of the module embedded in networks, which may be accentuated by the ambient network. This provides new insights into the functioning of such enzymatic modules individually and as part of networks, with relevance to other enzymatic signalling modules as well.

Description: We report high-resolution photoelectron spectra of the transition metal suboxide clusters Fe 3 O − and Co 3 O − . The combination of slow electron velocity-map imaging and cryogenic cooling yields vibrationally well-resolved spectra, from which we obtain precise values of 1.4408(3) and 1.3951(4) eV for the electron affinities of Fe 3 O and Co 3 O. Several vibrational frequencies of the neutral ground state Fe 3 O and Co 3 O clusters are assigned for the first time, and a low-lying excited state of Fe 3 O is observed. The experimental results are compared with density functional electronic structure calculations and Franck-Condon spectral simulations, enabling identification of the structural isomer and electronic states. As has been found in photoelectron spectra of other trimetal oxo species, Fe 3 O 0/− and Co 3 O 0/− are assigned to a μ 2 -oxo isomer with planar C 2 v symmetry. We identify the ground states of Fe 3 O – and Co 3 O – as 12 A 1 and 9 B 2 states, respectively. From these states we observe photodetachment to the 11 B 2 ground and 13 A 1 excited states of Fe 3 O, as well as to the 8 A 1 ground state of Co 3 O.

Description: Liquid helium nanodroplets, consisting of on average 2 × 10 6 atoms, are examined using femtosecond time-resolved photoelectron imaging. The droplets are excited by an extreme ultraviolet light pulse centered at 23.7 eV photon energy, leading to states within a band that is associated with the 1 s 3 p and 1 s 4 p Rydberg levels of free helium atoms. The initially excited states and subsequent relaxation dynamics are probed by photoionizing transient species with a 3.2 eV pulse and using velocity map imaging to measure time-dependent photoelectron kinetic energy distributions. Significant differences are seen compared to previous studies with a lower energy (1.6 eV) probe pulse. Three distinct time-dependent signals are analyzed by global fitting. A broad intense signal, centered at an electron kinetic energy (eKE) of 2.3 eV, grows in faster than the experimental time resolution and decays in ∼100 fs. This feature is attributed to the initially excited droplet state. A second broad transient feature, with eKE ranging from 0.5 to 4 eV, appears at a rate similar to the decay of the initially excited state and is attributed to rapid atomic reconfiguration resulting in Franck-Condon overlap with a broader range of cation geometries, possibly involving formation of a Rydberg-excited (He n )* core within the droplet. An additional relaxation pathway leads to another short-lived feature with vertical binding energies ≳2.4 eV, which is identified as a transient population within the lower-lying 1 s 2 p Rydberg band. Ionization at 3.2 eV shows an enhanced contribution from electronically excited droplet states compared to ejected Rydberg atoms, which dominate at 1.6 eV. This is possibly the result of increased photoelectron generation from the bulk of the droplet by the more energetic probe photons.

Description: Recent experiments indicate a connection between the structure of amyloid aggregates and their cytotoxicity as related to neurodegenerative diseases. Of particular interest is the Iowa Mutant, which causes early-onset of Alzheimer's disease. While wild-type Amyloid β -peptides form only parallel beta-sheet aggregates, the mutant also forms meta-stable antiparallel beta sheets. Since these structural variations may cause the difference in the pathological effects of the two A β -peptides, we have studied in silico the relative stability of the wild type and Iowa mutant in both parallel and antiparallel forms. We compare regular molecular dynamics simulations with such where the viscosity of the samples is reduced, which, we show, leads to higher sampling efficiency. By analyzing and comparing these four sets of all-atom molecular dynamics simulations, we probe the role of the various factors that could lead to the structural differences. Our analysis indicates that the parallel forms of both wild type and Iowa mutant aggregates are stable, while the antiparallel aggregates are meta-stable for the Iowa mutant and not stable for the wild type. The differences result from the direct alignment of hydrophobic interactions in the in-register parallel oligomers, making them more stable than the antiparallel aggregates. The slightly higher thermodynamic stability of the Iowa mutant fibril-like oligomers in its parallel organization over that in antiparallel form is supported by previous experimental measurements showing slow inter-conversion of antiparallel aggregates into parallel ones. Knowledge of the mechanism that selects between parallel and antiparallel conformations and determines their relative stability may open new avenues for the development of therapies targeting familial forms of early-onset Alzheimer's disease.

Description: Using the recently developed explicitly correlated coupled cluster method in connection with the aug-cc-pVTZ basis set, we generated the three-dimensional potential energy surface (3D-PES) of the ground state of the Ar–BeO complex. This PES covers the regions of the global and local minima, the saddle point, and the dissociation of the complex. The PES is also used for the calculation of the rovibrational spectrum up to the dissociation limit. The high density of levels which is observed favors the mixing of the states and hence the occurrence of anharmonic resonances. The wavefunctions of the high rovibrational levels exhibit large amplitude motions in addition to strong anharmonic resonances. Our theoretical spectrum should be helpful in identifying the van der Waals modes of this complex in laboratory.

Description: Fluctuating hydrodynamics (FHD) is a general framework of mesoscopic modeling and simulation based on conservational laws and constitutive equations of linear and nonlinear responses. However, explicit representation of electrical forces in FHD has yet to appear. In this work, we devised an Ansatz for the dynamics of dipole moment densities that is linked with the Poisson equation of the electrical potential ϕ in coupling to the other equations of FHD. The resulting ϕ-FHD equations then serve as a platform for integrating the essential forces, including electrostatics in addition to hydrodynamics, pressure-volume equation of state, surface tension, and solvent-particle interactions that govern the emergent behaviors of molecular systems at an intermediate scale. This unique merit of ϕ-FHD is illustrated by showing that the water dielectric function and ion hydration free energies in homogeneous and heterogenous systems can be captured accurately via the mesoscopic simulation. Furthermore, we show that the field variables of ϕ-FHD can be mapped from the trajectory of an all-atom molecular dynamics simulation such that model development and parametrization can be based on the information obtained at a finer-grained scale. With the aforementioned multiscale capabilities and a spatial resolution as high as 5 Å, the ϕ-FHD equations represent a useful semi-explicit solvent model for the modeling and simulation of complex systems, such as biomolecular machines and nanofluidics.

Description: The atomic structure and the electron transfer properties of hydrogen bonds formed between two carboxylated alkanethiol molecules connected to gold electrodes are investigated by employing the non-equilibrium Green's function formalism combined with density functional theory. Three types of molecular junctions are constructed, in which one carboxyl alkanethiol molecule contains two methylene, –CH 2 , groups and the other one is composed of one, two, or three –CH 2 groups. Our calculations show that, similarly to the cases of isolated carboxylic acid dimers, in these molecular junctions the two carboxyl, –COOH, groups form two H-bonds resulting in a cyclic structure. When self-interaction corrections are explicitly considered, the calculated transmission coefficients of these three H-bonded molecular junctions at the Fermi level are in good agreement with the experimental values. The analysis of the projected density of states confirms that the covalent Au–S bonds localized at the molecule-electrode interfaces and the electronic coupling between –COOH and S dominate the low-bias junction conductance. Following the increase of the number of the –CH 2 groups, the coupling between –COOH and S decreases deeply. As a result, the junction conductance decays rapidly as the length of the H-bonded molecules increases. These findings not only provide an explanation to the observed distance dependence of the electron transfer properties of H-bonds, but also help the design of molecular devices constructed through H-bonds.

Description: The treatment of bending and buckling of stiff biopolymer filaments by the popular worm-like chain model does not provide adequate understanding of these processes at the microscopic level. Thus, we have used the atomistic molecular-dynamic simulations and the Amber03 force field to examine the compression buckling of α-helix (AH) filaments at room temperature. It was found that the buckling instability occurs in AHs at the critical force f c in the range of tens of pN depending on the AH length. The decrease of the force f c with the contour length follows the prediction of the classic thin rod theory. At the force f c the helical filament undergoes the swift and irreversible transition from the smoothly bent structure to the buckled one. A sharp kink in the AH contour arises at the transition, accompanied by the disruption of the hydrogen bonds in its vicinity. The kink defect brings in an effective softening of the AH molecule at buckling. Nonbonded interactions between helical branches drive the rearrangement of a kinked AH into the ultimate buckled structure of a compact helical hairpin described earlier in the literature.

Description: The strong field ionization rates for ethylene, trans 1,3-butadiene, and trans,trans 1,3,5-hexatriene have been calculated using time-dependent configuration interaction with single excitations and a complex absorbing potential (TDCIS-CAP). The calculations used the aug-cc-pVTZ basis set with a large set of diffuse functions (3 s , 2 p , 3 d , and 1 f ) on each atom. The absorbing boundary was placed 3.5 times the van der Waals radius from each atom. The simulations employed a seven-cycle cosine squared pulse with a wavelength of 800 nm. Ionization rates were calculated for intensities ranging from 0.3 × 10 14 W/cm 2 to 3.5 × 10 14 W/cm 2 . Ionization rates along the molecular axis increased markedly with increasing conjugation length. By contrast, ionization rates perpendicular to the molecular axis were almost independent of the conjugation length.

Description: During the dissociative adsorption on a solid surface, the substrate usually participates in a passive manner to accommodate fragments produced upon the cleavage of the internal bond(s) of a (transient) molecular adsorbate. This simple picture, however, neglects the flexibility of surface atoms. Here, we report a Density Functional Theory study to revisit our early studies of the dissociative adsorption of CH 3 X (X = Br and Cl) on Si(100). We have identified a new reaction pathway, which involves a flip of a silicon dimer; this new pathway agrees better with experiments. For our main exemplar of CH 3 Br, insights have been gained using a simple model that involves a three-atom reactive center, Br-C-Si. When the silicon dimer flips, the interaction between C and Si in the Br-C-Si center is enhanced, evident in the increased energy-split of the frontier orbitals. We also examine how the dissociation dynamics of CH 3 Br is altered on a heterodimer (Si-Al, Si-P, and Si-Ge) in a Si(100) surface. In each case, we conclude, on the basis of computed reaction pathways, that no heterodimer flipping is involved before the system transverses the transition state to dissociative adsorption.

Description: The interface between Ru(tcterpy)(NCS) 3 TBA 2 [black dye (BD); tcterpy = 4,4 ′ ,4 ″ -tricarboxy-2,2 ′ :6 ′ ,2 ″ -terpyridine, NCS = thiocyanato, TBA = tetrabutylammonium cation] and nanocrystalline TiO 2 , as found in dye-sensitized solar cells, is investigated by soft-X-ray synchrotron radiation and compared with the adsorption structure of cis -Ru(Hdcbpy) 2 (NCS) 2 TBA 2 (N719; dcbpy = 4,4 ′ -dicarboxy-2,2 ′ -bipyridine) on TiO 2 to elucidate the relationship between the adsorption mode of BD and the photocurrent with and without coadsorbed indoline dye D131. The depth profile is characterized with X-ray photoelectron spectroscopy and S K -edge X-ray absorption fine structure using synchrotron radiation. Both datasets indicate that one of the isothiocyanate groups of BD interacts with TiO 2 via its S atom when the dye is adsorbed from a single-component solution. In contrast, the interaction is slightly suppressed when D131 is coadsorbed, indicated by the fact that the presence of D131 changes the adsorption mode of BD. Based upon these results, the number of BD dye molecules interacting with the substrate is shown to decrease by 10% when D131 is coadsorbed, and the dissociation is shown to be related to the short-circuit photocurrent in the 600–800 nm region. The design of a procedure to promote the preferential adsorption of D131 therefore leads to an improvement of the short-circuit current and conversion efficiency.

Description: We demonstrate that the Hadwiger form of the free energy of a fluid in contact with a wall is insufficient to describe the low-density behavior of a hard-sphere fluid. This implies that morphological thermodynamics of the hard-sphere fluid is an approximate theory if only four geometric measures are included. In order to quantify deviations from the Hadwiger form we extend standard fundamental measure theory of the bulk fluid by introducing additional scaled-particle variables which allow for the description of non-Hadwiger coefficients. The theory is in excellent agreement with recent computer simulations. The fact that the leading non-Hadwiger coefficient is one order of magnitude smaller than the smallest Hadwiger coefficient lends confidence to the numerous results that have been previously obtained within standard morphological thermodynamics.

Description: The development of a round liquid jet under the influence of a confined coaxial flow of an immiscible liquid of comparable density (central to annular flow density ratio of 8:10) was investigated in the vicinity of the nozzle exit. Two flow regimes were considered; one where the annular flow is faster than the central jet, so the central liquid jet is accelerated and one where the annular flow is slower, so the central liquid jet is decelerated. The central jet was visualised by high speed photography. Three modes of jet development were identified and classified in terms of the Reynolds number, Re, of the central jet which was in the range of 525 〈 Re 〈 2725, a modified definition of the Weber number, We, which allows the distinction between accelerating and deceleration flows and was in the range of −22 〈 We 〈 67 and the annular to central Momentum Ratio, MR, of the two streams which was in the range of 3.6 〈 MR 〈 91. By processing the time resolved jet images using Proper Orthogonal Decomposition (POD), it was possible to reduce the description of jet morphology to a small number of spatial modes, which isolated the most significant morphologies of the jet development. In this way, the temporal and spatial characteristics of the instabilities on the interface were clearly identified which highlights the advantages of POD over direct observation of the images. Relationships between the flow parameters and the interfacial waves were established. The wavelength of the interfacial instability was found to depend on the velocity of the fastest moving stream, which is contrary to findings for fluids with large density differences.

Description: Interaction of a vortex ring impinging on multiple permeable screens orthogonal to the ring axis was studied to experimentally investigate the persistence and decay of vortical structures inside the screen array using digital particle image velocimetry in a refractive index matched environment. The permeable screens had porosities (open area ratios) of 83.8%, 69.0%, and 55.7% and were held by a transparent frame that allowed the screen spacing to be changed. Vortex rings were generated using a piston-cylinder mechanism at nominal jet Reynolds numbers of 1000, 2000, and 3000 with piston stroke length-to-diameter ratios of 2 and 3. The interaction of vortex rings with the porous medium showed a strong dependence of the overall flow evolution on the screen porosity, with a central flow being preserved and vortex ring-like structures (with smaller diameter than the primary vortex ring) being generated near the centerline. Due to the large rod size used in the screens, immediate reformation of the transmitted vortex ring with size comparable to the primary ring (as has been observed with thin screens) was not observed in most cases. Since the screens have lower complexity and high open area ratios, centerline vortex ring-like flow structures formed with comparable size to the screen pore size and penetrated through the screens. In the case of low porosity screens (55.7%) with large screen spacing, re-emergence of large scale (large separation), weak vortical structures/pairs (analogous to a transmitted vortex ring) was observed downstream of the first screen. Additional smaller scale vortical structures were generated by the interaction of the vortex ring with subsequent screens. The size distribution of the generated vortical structures were shown to be strongly affected by porosity, with smaller vortical structures playing a stronger role as porosity decreased. Finally, porosity significantly affected the decay of total energy, but the effect of screen spacing decreased as porosity decreased.

Description: The explicit form of the zeroth Green's function in the Hückel model, approximated by the negative of the inverse of the Hückel matrix, has direct quantum interference consequences for molecular conductance. We derive a set of rules for transmission between two electrodes attached to a polyene, when the molecule is extended by an even number of carbons at either end (transmission unchanged) or by an odd number of carbons at both ends (transmission turned on or annihilated). These prescriptions for the occurrence of quantum interference lead to an unexpected consequence for switches which realize such extension through electrocyclic reactions: for some specific attachment modes the chemically closed ring will be the ON position of the switch. Normally the signs of the entries of the Green's function matrix are assumed to have no physical significance; however, we show that the signs may have observable consequences. In particular, in the case of multiple probe attachments – if coherence in probe connections can be arranged – in some cases new destructive interference results, while in others one may have constructive interference. One such case may already exist in the literature.

Description: Vortex cavitation forming in the leading-edge vortices of a delta wing was examined to determine how the individual cavitation bubbles incepted, grew, interacted with the underlying vortical flow and produced acoustic tones. The non-cavitating vortical flow over the delta wing was chosen to be similar to those previously reported in the literature. It was found that vortex breakdown was unaffected by the presence of incipient and developed vortex cavitation bubbles in the vortex core. While some cavitation bubbles incepted, grew, and collapsed relatively quickly, others reached an equilibrium position wherein the bubble tip was stationary in the laboratory frame at a particular location along the vortex axis. For a given attack angle, the equilibrium location moved upstream with a reduction in free stream cavitation number. It is shown that the existence of these stationary vortex bubbles is possible when there is a balance between the axial growth of the bubble along the vortex axis and the opposite motion of the axial jetting flow in the vortex core, and only a single equilibrium position is possible along the axially evolving vortex for a given free stream cavitation number. These transient and stationary vortex bubbles emit significant cavitation noise upon inception, growth, and collapse. The spectral content of the noise produced was expected to be related to the interaction of the bubble with the surrounding vortical flow in a manner similar to that reported in previous studies, where sustained tones were similar to the underlying vortex frequency. However, in the present study, the dominant frequency and higher harmonics of the tones occur at a higher frequency than that of the underlying vortex. Hence, it is likely that the highly elongated stationary bubbles have higher-order volume oscillations compared to the two-dimensional radial mode of the vortex cores of vortex cavitation bubbles with much smaller diameter-to-length ratios.

Description: Sustainable water management (SWM) requires allocating between competing water sector demands, and balancing the financial and social resources required to support necessary water systems. The objective of this review is to assess SWM in three sectors: urban, agricultural, and natural systems. This review explores the following questions: (1) How is SWM defined and evaluated? (2) What are the challenges associated with sustainable development in each sector? (3) What are the areas of greatest potential improvement in urban and agricultural water management systems? And (4) What role does country development status have in SWM practices? The methods for evaluating water management practices range from relatively simple indicator methods to integration of multiple models, depending on the complexity of the problem and resources of the investigators. The two key findings and recommendations for meeting SWM objectives are: (1) all forms of water must be considered usable, and reusable, water resources; and (2) increasing agricultural crop water production represents the largest opportunity for reducing total water consumption, and will be required to meet global food security needs. The level of regional development should not dictate sustainability objectives, however local infrastructure conditions and financial capabilities should inform the details of water system design and evaluation.

Description: We present a computational scheme for orbital-free density functional theory (OFDFT) that simultaneously provides access to all-electron values and preserves the OFDFT linear scaling as a function of the system size. Using the projector augmented-wave method (PAW) in combination with real-space methods, we overcome some obstacles faced by other available implementation schemes. Specifically, the advantages of using the PAW method are twofold. First, PAW reproduces all-electron values offering freedom in adjusting the convergence parameters and the atomic setups allow tuning the numerical accuracy per element. Second, PAW can provide a solution to some of the convergence problems exhibited in other OFDFT implementations based on Kohn-Sham (KS) codes. Using PAW and real-space methods, our orbital-free results agree with the reference all-electron values with a mean absolute error of 10 meV and the number of iterations required by the self-consistent cycle is comparable to the KS method. The comparison of all-electron and pseudopotential bulk modulus and lattice constant reveal an enormous difference, demonstrating that in order to assess the performance of OFDFT functionals it is necessary to use implementations that obtain all-electron values. The proposed combination of methods is the most promising route currently available. We finally show that a parametrized kinetic energy functional can give lattice constants and bulk moduli comparable in accuracy to those obtained by the KS PBE method, exemplified with the case of diamond.

Description: The Fenna-Matthews-Olson (FMO) protein-pigment complex acts as a molecular wire conducting energy between the outer antenna system and the reaction center; it is an important photosynthetic system to study the transfer of excitonic energy. Recent crystallographic studies report the existence of an additional (eighth) bacteriochlorophyll a (BChl a ) in some of the FMO monomers. To understand the functionality of this eighth BChl, we simulated the two-dimensional electronic spectra of both the 7-site ( apo form) and the 8-site ( holo form) variant of the FMO complex from green sulfur bacteria, Prosthecochloris aestuarii . By comparing the spectrum, it was found that the eighth BChl can affect two different excitonic energy transfer pathways: (1) it is directly involved in the first apo form pathway (6 → 3 → 1) by passing the excitonic energy to exciton 6; and (2) it facilitates an increase in the excitonic wave function overlap between excitons 4 and 5 in the second pathway (7 → 4,5 → 2 → 1) and thus increases the possible downward sampling routes across the BChls.

Description: The co-existence of disparate time scales is pervasive in many systems. In particular for surface reactions, it has been shown that the long-term evolution of the core oscillator is decisively influenced by slow surface changes, such as progressing deactivation. Here we present an in-depth numerical investigation of the coupled slow and fast surface dynamics in an electrocatalytic oscillator. The model consists of four nonlinear coupled ordinary differential equations, investigated over a wide parameter range. Besides the conventional bifurcation analysis, the system was studied by means of high-resolution period and Lyapunov diagrams. It was observed that the bifurcation diagram changes considerably as the irreversible surface poisoning evolves, and the oscillatory region shrinks. The qualitative dynamics changes accordingly and the chaotic oscillations are dramatically suppressed. Nevertheless, periodic cascades are preserved in a confined region of the resistance vs. voltage diagram. Numerical results are compared to experiments published earlier and the latter reinterpreted. Finally, the comprehensive description of the time-evolution in the period and Lyapunov diagrams suggests further experimental studies correlating the evolution of the system's dynamics with changes of the catalyst structure.

Description: Laminar flow over a periodic array of cylindrical surface roughness elements is simulated with an immersed boundary spectral method both to validate the method for subsequent studies and to examine how persistent streamwise vortices are introduced by a low Reynolds number roughness element. Direct comparisons are made with prior studies at a roughness-based Reynolds number Re k (= U ( k ) k / ν ) of 205 and a diameter to spanwise spacing ratio d / λ of 1/3. Downstream velocity contours match present and past experiments very well. The shear layer developed over the top of the roughness element produces the downstream velocity deficit. Upstream of the roughness element, the vortex topology is found to be consistent with juncture flow experiments, creating three cores along the recirculation line. Streamtraces stemming from these upstream cores, however, have unexpectedly little effect on the downstream flowfield as lateral divergence of the boundary layer quickly dissipates their vorticity. Long physical relaxation time of the recirculating wake behind the roughness remains a prominent issue for simulating this type of flowfield.

Description: We have recorded the complete infrared spectrum of methane 12 CH 4 and its second most abundant isotopomer 13 CH 4 extending from the fundamental range starting at 1000 cm −1 up to the overtone region near 12 000 cm −1 in the near infrared at the limit towards the visible range, at temperatures of about 80 K and also at 298 K with Doppler limited resolution in the gas phase by means of interferometric Fourier transform spectroscopy using the Bruker IFS 125 HR prototype (ZP 2001) of the ETH Zürich laboratory. This provides the so far most complete data set on methane spectra in this range at high resolution. In the present work we report in particular those results, where the partial rovibrational analysis allows for the direct assignment of pure ( J = 0) vibrational levels including high excitation. These results substantially extend the accurate knowledge of vibrational band centers to higher energies and provide a benchmark for both the comparison with theoretical results on the one hand and atmospheric spectroscopy on the other hand. We also present a simple effective Hamiltonian analysis, which is discussed in terms of vibrational level assignments and 13 C isotope effects.

Description: We report a molecular-dynamics simulation of a single-component system of particles interacting via a spherically symmetric potential that is found to form, upon cooling from a liquid state, a low-density porous crystalline phase. Its structure analysis demonstrates that the crystal can be described by a net with a topology that belongs to the class of topologies characteristic of the Metal-Organic Frameworks (MOFs). The observed net is new, and it is now included in the Reticular Chemistry Structure Resource database. The observation that a net topology characteristic of MOF crystals, which are known to be formed by a coordination-driven self-assembly process, can be reproduced by a thermodynamically stable configuration of a simple single-component system of particles opens a possibility of using these models in studies of MOF nets. It also indicates that structures with MOF topology, as well as other low-density porous crystalline structures can possibly be produced in colloidal systems of spherical particles, with an appropriate tuning of interparticle interaction.

Description: Electronically excited atom or molecule in an environment can relax via transferring its excess energy to the neighboring atoms or molecules. The process is called Interatomic or Intermolecular coulombic decay (ICD). The ICD is a fast decay process in environment. Generally, the ICD mechanism predominates in weakly bound clusters. In this paper, we have applied the complex absorbing potential approach/equation-of-motion coupled cluster (CAP/EOMCCSD) method which is a combination of CAP and EOMCC approach to study the lifetime of ICD at various geometries of the molecules. We have applied this method to calculate the lifetime of ICD in Ne-X; X = Ne, Mg, Ar, systems. We compare our results with other theoretical and experimental results available in literature.

Description: We present a computational study on HIO 2 molecules. Ground state properties such as equilibrium structures, relative energetics, vibrational frequencies, and infrared intensities were obtained for all the isomers at the coupled-cluster with single and double excitations as well as perturbative inclusion of triples (CCSD(T)) level of theory with the aug-cc-pVTZ-PP basis set and ECP-28-PP effective core potential for iodine and the aug-cc-pVTZ basis set for hydrogen and oxygen atoms. The HOIO structure is confirmed as the lowest energy isomer. The relative energies are shown to be HOIO 〈 HOOI 〈 HI(O)O. The HO(O)I isomer is only stable at the density functional theory (DFT) level of theory. The transition states determined show interconversion of the isomers is possible. In order to facilitate future experimental identification, vibrational frequencies are also determined for all corresponding deuterated species. Vertical excitation energies for the three lowest-lying singlet and triplet excited states were determined using the configuration interaction singles, time-dependent density functional theory (TD-DFT)/B3LYP, TD-DFT/G96PW91, and equation of motion-CCSD approaches with the LANL2DZ basis set plus effective core potential for iodine and the aug-cc-pVTZ basis set for hydrogen and oxygen atoms. It is shown that HOIO and HOOI isomers have excited states accessible at solar wavelengths (

Description: Symmetry breaking caused by geometric fluctuations can enable processes that are otherwise forbidden. An example is a perylene bisimide dyad whose dipole moments are perpendicular to each other. Förster-type energy transfer is thus forbidden at the equilibrium geometry since the dipolar coupling vanishes. Yet, fluctuations of the geometric arrangement have been shown to induce finite energy transfer that depends on the dipole variance, rather than the mean. We demonstrate an analogous effect associated with chirality symmetry breaking. In its equilibrium geometry, this dimer is non-chiral. The linear chiral response which depends on the average geometry thus vanishes. However, we show that certain 2D chiral optical signals are finite due to geometric fluctuations. Furthermore, the correlation time of these fluctuations can be experimentally revealed by the waiting time dependence of the 2D signal.

Description: We extend the periodic von Neumann basis to non-Cartesian coordinates. The bound states of two isomerizing triatomic molecules, LiCN/LiNC and HCN/HNC, are calculated using the vibrational Hamiltonian in Jacobi coordinates. The phase space localization of the basis functions leads to a flexible and accurate representation of the Hamiltonian. This results in significant savings compared to a basis localized just in coordinate space. The favorable scaling of the method with dimensionality makes it promising for applications to larger systems.

Description: Following the recent identification of ethanethiol in the interstellar medium (ISM) we have carried out Vacuum UltraViolet (VUV) spectroscopy studies of ethanethiol (CH 3 CH 2 SH) from 10 K until sublimation in an ultrahigh vacuum chamber simulating astrochemical conditions. These results are compared with those of methanethiol (CH 3 SH), the lower order thiol also reported to be present in the ISM. VUV spectra recorded at higher temperature reveal conformational changes in the ice and phase transitions whilst evidence for dimer production is also presented.

Description: The parallel components of static electric dipole polarizabilities have been calculated for the lowest lying spin-orbit states of the penta- and hexavalent oxidation states of the actinides (An) U, Np, and Pu, in both their atomic and molecular diyl ion forms (An 5+/6+ and AnO 2 +/2+ ) using the numerical finite-field technique within a four-component relativistic framework. The four-component Dirac-Hartree-Fock method formed the reference for MP2 and CCSD(T) calculations, while multireference Fock space coupled-cluster (FSCC), intermediate Hamiltonian Fock space coupled-cluster (IH-FSCC) and Kramers restricted configuration interaction (KRCI) methods were used to incorporate additional electron correlation. It is observed that electron correlation has significant (∼5 a.u. 3 ) impact upon the parallel component of the polarizabilities of the diyls. To the best of our knowledge, these quantities have not been previously reported and they can serve as reference values in the determination of various electronic and response properties (for example intermolecular forces, optical properties, etc.) relevant to the nuclear fuel cycle and material science applications. The highest quality numbers for the parallel components (α zz ) of the polarizability for the lowest Ω levels corresponding to the ground electronic states are (in a.u. 3 ) 44.15 and 41.17 for UO 2 + and UO 2 2+ , respectively, 45.64 and 41.42 for NpO 2 + and NpO 2 2+ , respectively, and 47.15 for the PuO 2 + ion.

Description: DNA-binding proteins locate and bind their target sequences positioned on DNA in crowded environments, but the molecular crowding effect on this search process is not clear. Using analytical techniques and Langevin dynamics simulations in two dimensions (2D), we find that the essential physics for facilitated diffusion in 2D search and 3D search is the same. We observe that the average search times have minima at the same optimal nonspecific binding energy for the cases with and without the crowding particle. Moreover, the molecular crowding increases the search time by increasing the average search rounds and the one-dimensional (1D) sliding time of a round, but almost not changing the average 2D diffusion time of a round. In addition, the fraction of 1D sliding time out of the total search time increases with increasing the concentration of crowders. For 2D diffusion, the molecular crowding decreases the jumping length and narrows its distribution due to the cage effect from crowders. These results shed light on the role of facilitated diffusion in DNA targeting kinetics in living cells.

Description: Protein conformation and orientation in the lipid membrane plays a key role in many cellular processes. Here we use molecular dynamics simulation to investigate the relaxation and C-terminus diffusion of a model helical peptide: beta-amyloid (Aβ) in a lipid membrane. We observed that after the helical peptide was initially half-embedded in the extracelluar leaflet of phosphatidylcholine (PC) or PC/cholesterol (PC/CHOL) membrane, the C-terminus diffused across the membrane and anchored to PC headgroups of the cytofacial lipid leaflet. In some cases, the membrane insertion domain of the Aβ was observed to partially unfold. Applying a sigmoidal fit to the process, we found that the characteristic velocity of the C-terminus, as it moved to its anchor site, scaled with θ u −4/3 , where θ u is the fraction of the original helix that was lost during a helix to coil transition. Comparing this scaling with that of bead-spring models of polymer relaxation suggests that the C-terminus velocity is highly regulated by the peptide helical content, but that it is independent of the amino acid type. The Aβ was stabilized by the attachment of the positive Lys28 side chain to the negative phosphate of PC or 3β oxygen of CHOL in the extracellular lipid leaflet and of the C-terminus to its anchor site in the cytofacial lipid leaflet.

Description: Ordering phenomena have been investigated in liquid Al–Zn alloys performing molecular dynamics (MD) simulations using “empirical oscillating pair potentials.” The local structural order is studied by computing two microscopic functions, namely, the concentration fluctuation function and the Warren-Cowley short-range order parameter. We also study the influence of ordering phenomena on transport properties like diffusivity and viscosity. The MD results are confronted to those determined from measurements and in the framework of the quasi-lattice theory.

Description: “Spin-forbidden” transitions are calculated for an eight-membered set of iridium-containing candidate molecules for organic light-emitting diodes (OLEDs) using two-component time-dependent density functional theory. Phosphorescence lifetimes (obtained from averaging over relevant excitations) are compared to experimental data. Assessment of parameters like non-distorted and distorted geometric structures, density functionals, relativistic Hamiltonians, and basis sets was done by a thorough study for Ir(ppy) 3 focussing not only on averaged phosphorescence lifetimes, but also on the agreement of the triplet substate structure with experimental data. The most favorable methods were applied to an eight-membered test set of OLED candidate molecules; Boltzmann-averaged phosphorescence lifetimes were investigated concerning the convergence with the number of excited states and the changes when including solvent effects. Finally, a simple model for sorting out molecules with long averaged phosphorescence lifetimes is developed by visual inspection of computationally easily achievable one-component frontier orbitals.

Description: We present a general formalism where different levels of coupled cluster theory can be applied to different parts of the molecular system. The system is partitioned into subsystems by Cholesky decomposition of the one-electron Hartree-Fock density matrix. In this way the system can be divided across chemical bonds without discontinuities arising. The coupled cluster wave function is defined in terms of cluster operators for each part and these are determined from a set of coupled equations. The total wave function fulfills the Pauli-principle across all borders and levels of electron correlation. We develop the associated response theory for this multi-level coupled cluster theory and present proof of principle applications. The formalism is an essential tool in order to obtain size-intensive complexity in the calculation of local molecular properties.

Description: We study the role of dispersion and electrostatic interactions in the wetting behavior of ionic liquids on non-ionic solid substrates. We consider a simple model of an ionic liquid consisting of spherical ions that interact via Lennard-Jones and Coulomb potentials. Bulk and interfacial properties are computed for five fluids distinguished by the strength of the electrostatic interaction relative to the dispersion interaction. We employ Monte Carlo simulations and an interface-potential-based approach to calculate the liquid-vapor and substrate-fluid interfacial properties. Surface tensions for each fluid are evaluated over a range of temperatures that spans from a reduced temperature of approximately 0.6 to the critical point. Contact angles are calculated at select temperatures over a range of substrate-fluid interaction strengths that spans from the near-drying regime to the wetting regime. We observe that an increase in the relative strength of Coulombic interactions between ions leads to increasing deviation from Guggenheim's corresponding states theory. We show how this deviation is related to lower values of liquid-vapor excess entropies observed for strongly ionic fluids. Our results show that the qualitative nature of wetting behavior is significantly influenced by the competition between dispersion and electrostatic interactions. We discuss the influence of electrostatic interactions on the nature of wetting and drying transitions and corresponding states like behavior observed for contact angles. For all of the fluids studied, we observe a relatively narrow range of substrate-fluid interaction strengths wherein the contact angle is nearly independent of temperature. The influence of the ionic nature of the fluid on the temperature dependence of contact angle is also discussed.

Description: We have recently been made aware by Prof. Sharon Megdal (The University of Arizona) and Dr. Peter Dillon (CSIRO) of some errors and omissions in our recent paper [1]. The authors wish to make the following corrections to this paper:[...]

Description: Since the time of Kirkwood, observed deviations in magnitude of the dielectric constant of aqueous protein solution from that of neat water (∼80) and slower decay of polarization have been subjects of enormous interest, controversy, and debate. Most of the common proteins have large permanent dipole moments (often more than 100 D) that can influence structure and dynamics of even distant water molecules, thereby affecting collective polarization fluctuation of the solution, which in turn can significantly alter solution's dielectric constant. Therefore, distance dependence of polarization fluctuation can provide important insight into the nature of biological water. We explore these aspects by studying aqueous solutions of four different proteins of different characteristics and varying sizes, chicken villin headpiece subdomain (HP-36), immunoglobulin binding domain protein G (GB1), hen-egg white lysozyme (LYS), and Myoglobin (MYO). We simulate fairly large systems consisting of single protein molecule and 20000–30000 water molecules (varied according to the protein size), providing a concentration in the range of ∼2–3 mM. We find that the calculated dielectric constant of the system shows a noticeable increment in all the cases compared to that of neat water. Total dipole moment auto time correlation function of water ⟨δ M W (0)δ M W ( t )⟩ is found to be sensitive to the nature of the protein. Surprisingly, dipole moment of the protein and total dipole moment of the water molecules are found to be only weakly coupled. Shellwise decomposition of water molecules around protein reveals higher density of first layer compared to the succeeding ones. We also calculate heuristic effective dielectric constant of successive layers and find that the layer adjacent to protein has much lower value (∼50). However, progressive layers exhibit successive increment of dielectric constant, finally reaching a value close to that of bulk 4–5 layers away. We also calculate shellwise orientational correlation function and tetrahedral order parameter to understand the local dynamics and structural re-arrangement of water. Theoretical analysis providing simple method for calculation of shellwise local dielectric constant and implication of these findings are elaborately discussed in the present work.

Description: This second paper in a series of two reports on the performance of a new instrument for studying chemical reaction dynamics and kinetics at low temperatures. Our approach employs chirped-pulse Fourier-transform microwave (CP-FTMW) spectroscopy to probe photolysis and bimolecular reaction products that are thermalized in pulsed uniform flows. Here we detail the development and testing of a new K a -band CP-FTMW spectrometer in combination with the pulsed flow system described in Paper I [J. M. Oldham, C. Abeysekera, B. Joalland, L. N. Zack, K. Prozument, I. R. Sims, G. B. Park, R. W. Field, and A. G. Suits, J. Chem. Phys.141, 154202 (2014)]. This combination delivers broadband spectra with MHz resolution and allows monitoring, on the μs timescale, of the appearance of transient reaction products. Two benchmark reactive systems are used to illustrate and characterize the performance of this new apparatus: the photodissociation of SO 2 at 193 nm, for which the vibrational populations of the SO product are monitored, and the reaction between CN and C 2 H 2 , for which the HCCCN product is detected in its vibrational ground state. The results show that the combination of these two well-matched techniques, which we refer to as chirped-pulse in uniform flow, also provides insight into the vibrational and rotational relaxation kinetics of the nascent reaction products. Future directions are discussed, with an emphasis on exploring the low temperature chemistry of complex polyatomic systems.

Description: We present molecular dynamics simulation results pertaining to the solvation of Li + in dimethyl sulfoxide-acetonitrile binary mixtures. The results are potentially relevant in the design of Li-air batteries that rely on aprotic mixtures as solvent media. To analyze effects derived from differences in ionic size and charge sign, the solvation of Li + is compared to the ones observed for infinitely diluted K + and Cl − species, in similar solutions. At all compositions, the cations are preferentially solvated by dimethyl sulfoxide. Contrasting, the first solvation shell of Cl − shows a gradual modification in its composition, which varies linearly with the global concentrations of the two solvents in the mixtures. Moreover, the energetics of the solvation, described in terms of the corresponding solute-solvent coupling, presents a clear non-ideal concentration dependence. Similar nonlinear trends were found for the stabilization of different ionic species in solution, compared to the ones exhibited by their electrically neutral counterparts. These tendencies account for the characteristics of the free energy associated to the stabilization of Li + Cl − , contact-ion-pairs in these solutions. Ionic transport is also analyzed. Dynamical results show concentration trends similar to those recently obtained from direct experimental measurements.

Description: Knowledge of how intermolecular interactions of amyloid-forming proteins cause protein aggregation and how those interactions are affected by sequence and solution conditions is essential to our understanding of the onset of many degenerative diseases. Of particular interest is the aggregation of the amyloid-β (Aβ) peptide, linked to Alzheimer's disease, and the aggregation of the Sup35 yeast prion peptide, which resembles the mammalian prion protein linked to spongiform encephalopathies. To facilitate the study of these important peptides, experimentalists have identified small peptide congeners of the full-length proteins that exhibit amyloidogenic behavior, including the KLVFFAE sub-sequence, Aβ 16−22 , and the GNNQQNY subsequence, Sup35 7−13 . In this study, molecular dynamics simulations were used to examine these peptide fragments encapsulated in reverse micelles (RMs) in order to identify the fundamental principles that govern how sequence and solution environment influence peptide aggregation. Aβ 16−22 and Sup35 7−13 are observed to organize into anti-parallel and parallel β-sheet arrangements. Confinement in the sodium bis(2-ethylhexyl) sulfosuccinate (AOT) reverse micelles is shown to stabilize extended peptide conformations and enhance peptide aggregation. Substantial fluctuations in the reverse micelle shape are observed, in agreement with earlier studies. Shape fluctuations are found to facilitate peptide solvation through interactions between the peptide and AOT surfactant, including direct interaction between non-polar peptide residues and the aliphatic surfactant tails. Computed amide I IR spectra are compared with experimental spectra and found to reflect changes in the peptide structures induced by confinement in the RM environment. Furthermore, examination of the rotational anisotropy decay of water in the RM demonstrates that the water dynamics are sensitive to the presence of peptide as well as the peptide sequence. Overall, our results demonstrate that the RM is a complex confining environment where substantial direct interaction between the surfactant and peptides plays an important role in determining the resulting ensemble of peptide conformations. By extension the results suggest that similarly complex sequence-dependent interactions may determine conformational ensembles of amyloid-forming peptides in a cellular environment.

Description: A suspension of charged colloidal silica spheres exhibiting a bi-modal size distribution of particles, thereby mimicking a binary mixture, was studied using time-resolved ultra-small-angle synchrotron X-ray scattering (USAXS). The sample, consisting of particles of diameters d A = (104.7 ± 9.0)  nm and d B = (88.1 ± 7.8)  nm ( d A / d B ≈ 1.2), and with an estimated composition A 0.6(1) B 0.4(1) , was studied with respect to its phase behaviour in dependance of particle number density and interaction, of which the latter was modulated by varying amounts of added base (NaOH). Moreover, its short-range order in the fluid state and its eventual solidification into a long-range ordered colloidal crystal were observed in situ , allowing the measurement of the associated kinetics of nucleation and crystal growth. Key parameters of the nucleation kinetics such as crystallinity, crystallite number density, and nucleation rate density were extracted from the time-resolved scattering curves. By this means an estimate on the interfacial energy for the interface between the icosahedral short-range ordered fluid and a body-centered cubic colloidal crystal was obtained, comparable to previously determined values for single-component colloidal systems.

Description: We developed an energetic model by integrating the generalized Langevin equation with the Cahn-Hilliard equation to simulate the diffusive behaviors of receptor proteins in the plasma membrane of a living cell. Simulation results are presented to elaborate the confinement effects from actin corrals and protein-induced lipid domains. Single-molecule tracking data of epidermal growth factor receptors (EGFR) acquired on live HeLa cells agree with the simulation results and the mechanism that controls the diffusion of single-molecule receptors is clarified. We discovered that after ligand binding, EGFR molecules move into lipid nanodomains. The transition rates between different diffusion states of liganded EGFR molecules are regulated by the lipid domains. Our method successfully captures dynamic interactions of receptors at the single-molecule level and provides insight into the functional architecture of both the diffusing EGFR molecules and their local cellular environment.

Description: The structure of the first layer CO adsorbed on NaCl(100) is investigated experimentally by means of quantitative low-energy electron diffraction at 25 K, and theoretically by means of density functional theory. Consistent with earlier helium atom diffraction results, the monolayer structure has p(2×1) symmetry with a glide-plane along the longer axis of the unit cell. The structure analysis confirms the binding of CO via the carbon end to the NaCl(100) surface. The vertical distance of carbon above Na + is 2.58 ± 0.08 Å, in good agreement with geometry optimizations based on dispersion-corrected density functional theory, and 0.15 Å lower than predicted in calculations based on the nonlocal van der Waals density functional.

Description: The valence band structure of α-phase crystalline films of cobalt phthalocyanine (CoPc) grown on Au(111) is investigated by using angle-resolved photoemission spectroscopy (ARPES) with synchrotron radiation. The photo-induced change in the ARPES peaks is noticed in shape and energy of the highest occupied molecular orbital (HOMO, C 2 p ) and HOMO-1 (Co 3 d ) of CoPc, and is misleading the interpretation of the electronic properties of CoPc films. From the damage-free normal-emission ARPES measurement, the clear valence-band dispersion has been first observed, showing that orbital-specific behaviors are attributable to the interplay of the intermolecular π-π and π-d interactions. The HOMO band dispersion of 0.1 eV gives the lower limit of the hole mobility for α-CoPc of 28.9 cm 2  V −1  s −1 at 15 K. The non-dispersive character of the split HOMO-1 bands indicates that the localization of the spin state is a possible origin of the antiferromagnetism.

Description: A five-dimensional potential energy surface (PES) for the interaction of a rigid methane molecule with a rigid nitrogen molecule was determined from quantum-chemical ab initio calculations. The counterpoise-corrected supermolecular approach at the CCSD(T) level of theory was utilized to compute a total of 743 points on the PES. The interaction energies were calculated using basis sets of up to quadruple-zeta quality with bond functions and were extrapolated to the complete basis set limit. An analytical site-site potential function with nine sites for methane and five sites for nitrogen was fitted to the interaction energies. The PES was validated by calculating the cross second virial coefficient as well as the shear viscosity and binary diffusion coefficient in the dilute-gas limit for CH 4 –N 2 mixtures. An improved PES was obtained by adjusting a single parameter of the analytical potential function in such a way that quantitative agreement with the most accurate experimental values of the cross second virial coefficient was achieved. The transport property values obtained with the adjusted PES are in good agreement with the best experimental data.

Description: Ultrastable glasses have risen to prominence due to their potentially useful material properties and the tantalizing possibility of a general method of preparation via vapor deposition. Despite the importance of this novel class of amorphous materials, numerical studies have been scarce because achieving ultrastability in atomistic simulations is an enormous challenge. Here, we bypass this difficulty and establish that randomly pinning the position of a small fraction of particles inside an equilibrated supercooled liquid generates ultrastable configurations at essentially no numerical cost, while avoiding undesired structural changes due to the preparation protocol. Building on the analogy with vapor-deposited ultrastable glasses, we study the melting kinetics of these configurations following a sudden temperature jump into the liquid phase. In homogeneous geometries, we find that enhanced kinetic stability is accompanied by large scale dynamic heterogeneity, while a competition between homogeneous and heterogeneous melting is observed when a liquid boundary invades the glass at constant velocity. Our work demonstrates the feasibility of large-scale, atomistically resolved, and experimentally relevant simulations of the kinetics of ultrastable glasses.

Description: We develop a numerical approach for simulating light-induced charge transport dynamics across a metal-molecule-metal conductance junction. The finite-difference time-domain method is used to simulate the plasmonic response of the metal structures. The Huygens subgridding technique, as adapted to Lorentz media, is used to bridge the vastly disparate length scales of the plasmonic metal electrodes and the molecular system, maintaining accuracy. The charge and current densities calculated with classical electrodynamics are transformed to an electronic wavefunction, which is then propagated through the molecular linker via the Heisenberg equations of motion. We focus mainly on development of the theory and exemplify our approach by a numerical illustration of a simple system consisting of two silver cylinders bridged by a three-site molecular linker. The electronic subsystem exhibits fascinating light driven dynamics, wherein the charge density oscillates at the driving optical frequency, exhibiting also the natural system timescales, and a resonance phenomenon leads to strong conductance enhancement.

Description: A new, four-dimensional potential energy surface for the interaction of NH 3 and ND 3 with Ar is computed using the coupled-cluster method with single, double, and perturbative triple excitations and large basis sets. The umbrella motion of the ammonia molecule is explicitly taken into account. The bound states of both NH 3 –Ar and ND 3 –Ar are calculated on this potential for total angular momentum values from J = 0 to 10, with the inclusion of Coriolis interactions. The energies and splittings of the rovibrational levels are in excellent agreement with the extensive high-resolution spectroscopic data accumulated over the years in the infrared and microwave regions for both complexes, which demonstrates the quality of the potential energy surface.

Description: We have systematically investigated the crystal structure of Ba-doped phenanthrene with various Ba doping levels by the first-principles calculations combined with the X-ray diffraction (XRD) spectra simulations. Although the experimental stoichiometry ratio of Ba atom and phenanthrene molecule is 1.5:1, the simulated XRD spectra, space group symmetry and optimized lattice parameters of Ba 1.5 phenanthrene are not consistent with the experimental ones, while the results for Ba 2 phenanthrene are in good agreement with the measurements. The strength difference of a few XRD peaks can be explained by the existence of pristine phenanthrene. Our findings suggest that instead of uniform Ba 1.5 phenanthrene, there coexist Ba 2 phenanthrene and undoped phenanthrene in the superconducting sample. The electronic calculations indicate that Ba 2 phenanthrene is a semiconductor with a small energy gap less than 0.05 eV.

Description: A new formalism for the accurate treatment of adiabatic effects in the hydrogen molecule is presented, in which the electronic wave function is expanded in the James-Coolidge basis functions. Systematic increase in the size of the basis set permits estimation of the accuracy. Numerical results for the adiabatic correction to the Born-Oppenheimer interaction energy reveal a relative precision of 10 −12 at an arbitrary internuclear distance. Such calculations have been performed for 88 internuclear distances in the range of 0 〈 R ⩽ 12 bohrs to construct the adiabatic correction potential and to solve the nuclear Schrödinger equation. Finally, the adiabatic correction to the dissociation energies of all rovibrational levels in H 2 , HD, HT, D 2 , DT, and T 2 has been determined. For the ground state of H 2 the estimated precision is 3 × 10 −7  cm −1 , which is almost three orders of magnitude higher than that of the best previous result. The achieved accuracy removes the adiabatic contribution from the overall error budget of the present day theoretical predictions for the rovibrational levels.

Description: Self-assembly of polyhedral-shaped particles has attracted huge interest with the advent of new synthesis methods that realize these faceted particles in the lab. Recent studies have shown that polyhedral-shaped particles exhibit a rich phase behavior by excluded volume interactions alone; some of these particles are even alleged to show a transition to a glass phase by quenching the liquid sufficiently fast beyond the glass transition (supercooling), such that the formation of structures with long-range order is suppressed. Despite the recent progress, no study has been made on the glass formation of polyhedral-shaped particles. Here, we study the glass behavior of polyhedral particles using advanced Monte Carlo methods. We investigate the formation of a glass of monodisperse hard polyhedral-shaped particles, namely, octahedra, tetrahedra, and triangular cupola, using simulations. Finally, the fragility of these particles is determined and compared to that of a polydisperse hard-sphere system.

Description: In this paper, we have studied the properties of a Brownian particle at stationary state in the presence of a fluctuating magnetic field. Time dependence of the field makes the system thermodynamically open. As a signature of that the steady state distribution function becomes function of damping strength, intensity of fluctuations and constant parts of the applied magnetic field. It also depends on the correlation time of the fluctuating magnetic field. Our another observation is that the random magnetic field can induce the resonant activation phenomenon. Here correlation time is increased under the fixed variance of the fluctuating field. But if the correlation time (τ) increases under the fixed field strength then the mean first passage time rapidly grows at low τ and it almost converges at other limit. This is sharp contrast to the usual colored noise driven open system case where the mean first passage time diverges exponentially. We have also observed that a giant enhancement of barrier crossing rate occurs particularly at large strength of constant parts of the applied magnetic field even for very weak fluctuating magnetic field. Finally, break down of the Arrhenius result and disappearance of the Kramers’ turn over phenomenon may occur in the presence of a fluctuating magnetic field.

Description: We present a novel approach to nucleation processes based on the GENERIC framework (general equation for the nonequilibrium reversible-irreversible coupling). Solely based on the GENERIC structure of time-evolution equations and thermodynamic consistency arguments of exchange processes between a metastable phase and a nucleating phase, we derive the fundamental dynamics for this phenomenon, based on continuous Fokker-Planck equations. We are readily able to treat non-isothermal nucleation even when the nucleating cores cannot be attributed intensive thermodynamic properties. In addition, we capture the dynamics of the time-dependent metastable phase being continuously expelled from the nucleating phase, and keep rigorous track of the volume corrections to the dynamics. Within our framework the definition of a thermodynamic nuclei temperature is manifest. For the special case of nucleation of a gas phase towards its vapor-liquid coexistence, we illustrate that our approach is capable of reproducing recent literature results obtained by more microscopic considerations for the suppression of the nucleation rate due to nonisothermal effects.

Description: Measures of soil and water conservation (SWC) could affect the hydrological process. The impacts of typical measures on groundwater recharge, levels and flow were analyzed based on simulated rainfall experiments and a groundwater model. The three-dimensional finite-difference groundwater flow model (MODFLOW) was calibrated and verified for bare slope, grassland and straw mulching scenarios based on the experiments. The results of the verification in groundwater balance, levels, runoff and flow field all showed that MODFLOW could be applied to study the impact of SWC measures on groundwater. Meanwhile, the results showed the recharge rate (α) and specific yield of the three soil layers (Sy1, Sy2 and Sy3) were the most sensitive parameters to the change in the underlying surface. Then, the impacts of the SWC measures’ construction and destruction on the groundwater regime were studied. The results indicated the measures could strengthen groundwater recharge. The amounts of groundwater recharge, runoff and level were on the order of straw mulching > grassland > bare slope. When the underlying surface was converted from grass and mulching to bare slope, the recharge decreased by 42.2% and 39.1%. It was concluded that SWC measure construction would increase groundwater recharge and the measure destruction would decrease recharge.

Description: The article “Characteristics of Point Recharge in Karst Aquifers, Water 6: 2782–2807” by N. Somaratne evaluates various recharge estimation techniques applied to four limestone aquifers in South Australia. Somaratne [1] concludes that methods based on watertable fluctuations, groundwater modelling and water budgets are independent of recharge processes, and are therefore superior to the chloride mass balance (CMB) approach for karst aquifers. The current comment offers alternative interpretations from existing field measurements and previous literature, in particular for the Uley South aquifer, which is the focus of much of the article by Somaratne [1]. Conclusions regarding this system are revised, partly to account for the misrepresentation of previous studies. The aeolianite sediments of Uley South are mostly unconsolidated or poorly consolidated, and dissolution features in the calcrete capping provide point infiltration into a predominantly unconsolidated vadose zone, whereas Somaratne’s [1] findings require that the system comprises well-developed conduits in otherwise low-conductivity limestone. Somaratne’s [1] assertion that the basic premise of CMB is violated in Uley South is disputable, given strong evidence of relatively well-mixed groundwater arising from mostly diffuse recharge. The characterization of karst aquifer recharge should continue to rely on multiple techniques, including environmental tracers such as chloride.

Description: This editorial provides an overview of the special issue “Wetlands and Sustainability”. In particular, the special issue contains a review of Paul Keddy’s book “Wetland Ecology” with specific reference to wetland sustainability. It also includes papers addressing wetland data acquisition via radar and remote sensing to better understand wetland system dynamics, hydrologic processes linked to wetland stress and restoration, coastal wetlands land use conflict/management, and wetland utilization for water quality treatment.

Description: Most of the waterborne disease outbreaks observed in North America are associated with rural drinking water systems. The majority of the reported waterborne outbreaks are related to microbial agents (parasites, bacteria and viruses). Rural areas are characterized by high livestock density and lack of advanced treatment systems for animal and human waste, and wastewater. Animal waste from livestock production facilities is often applied to land without prior treatment. Biosolids (treated municipal wastewater sludge) from large wastewater facilities in urban areas are often transported and applied to land in rural areas. This situation introduces a potential for risk of human exposure to waterborne contaminants such as human and zoonotic pathogens originating from manure, biosolids, and leaking septic systems. This paper focuses on waterborne outbreaks and sources of microbial pollution in rural areas in the US, characterization of the microbial load of biosolids and manure, association of biosolid and manure application with microbial contamination of surface and groundwater, risk assessment and best management practice for biosolids and manure application to protect water quality. Gaps in knowledge are identified, and recommendations to improve the water quality in the rural areas are discussed.

Description: The impact of climate change and Baltic Sea level rise on groundwater resources in a shallow, unconfined, low-lying coastal aquifer in Hanko, southern Finland, was assessed using the UZF1 model package coupled with the three-dimensional groundwater flow model MODFLOW to simulate flow from the unsaturated zone through the aquifer. The snow and PET models were used to calculate the surface water availability for infiltration from the precipitation data used in UZF1. Infiltration rate, flow in the unsaturated zone and groundwater recharge were then simulated using UZF1. The simulation data from climate and sea level rise scenarios were compared with present data. The results indicated changes in recharge pattern during 2071–2100, with recharge occurring earlier in winter and early spring. The seasonal impacts of climate change on groundwater recharge were more significant, with surface overflow resulting in flooding during winter and early spring and drought during summer. Rising sea level would cause some parts of the aquifer to be under sea level, compromising groundwater quality due to intrusion of sea water. This, together with increased groundwater recharge, would raise groundwater levels and consequently contribute more surface leakage and potential flooding in the low-lying aquifer.

Description: Solutal Marangoni instability (SMI) is investigated both in 2D and 3D using a combined Cahn-Hilliard and Navier-Stokes model in a finite system. Fe-Sn is chosen as a representative alloy system since the phase diagram reveals a region with a miscibility gap, where two liquid phases, namely, the Fe-rich phase L 1 and the Sn-rich phase L 2 , are in chemical equilibrium. In 3D, considering a perturbed liquid cylinder ( L 2 phase) with a length of λ and a radius of R 0 embedded in the middle of a simulation box of λ × H × H (length × width × height) surrounded by the phase L 1 , we find that the perturbation induced Marangoni flow is either clockwise or anti-clockwise depending on the mean curvature difference between the convex and concave regions which is affected by the ratio of λ/ R 0 . The critical ratio of λ/ R 0 for SMI is shown to be invariant for different Marangoni numbers as well as independent of the geometrical properties of the L 1 phase. In 2D, a perturbed liquid pipe with a length of λ and a radius of R 0 embedded in the middle of a simulation box of λ × H (length × height) is taken into account. Due to different curvature constitution, the critical ratio of λ/ R 0 for SMI depends on the height of the L 1 phase.

Description: For several years, a promising Plasma Synthetic Jet actuator for high-speed flow control has been under development at ONERA. So far, its confined geometry and small space-time scales at play have prevented its full experimental characterization. Complementary accurate numerical simulations are then considered in this study in order to provide a complete aerothermodynamic description of the actuator. Two major obstacles have to be overcome with this approach: the modeling of the energy deposited by the electric arc and the accurate computation of the transient response of the cavity generating the pulsed jet. To solve the first problem, an Euler solver coupled with an electric circuit model was used to evaluate the energy deposition in the cavity. Such a coupling is performed by considering the electric field between the two electrodes. The second issue was then addressed by injecting these source terms in large Eddy simulations of the entire actuator. Aerodynamic results were finally compared with Schlieren visualizations. Using the proposed methodology, the temporal evolution of the jet front is remarkably well predicted.

Description: Infrared photodissociation (IRPD) spectra of mass-selected 4-aminobenzonitrile-(water) n cluster cations, ABN + -(H 2 O) n with n ≤ 4, recorded in the N–H and O–H stretch ranges are analyzed by quantum chemical calculations at the M06-2X/aug-cc-pVTZ level to determine the evolution of the initial microhydration process of this bifunctional aromatic cation in its ground electronic state. IRPD spectra of cold clusters tagged with Ar and N 2 display higher resolution and allow for a clear-cut structural assignment. The clusters are generated in an electron impact source, which generates predominantly the most stable isomers. The IRPD spectra are assigned to single isomers for n = 1–3. The preferred cluster growth begins with sequential hydration of the two acidic NH protons of the amino group (n = 1–2), which is followed by attachment of secondary H 2 O ligands hydrogen-bonded to the first-shell ligands (n = 3–4). These symmetric and branched structures are more stable than those with a cyclic H-bonded solvent network. Moreover, in the size range n ≤ 4 the formation of a solvent network stabilized by strong cooperative effects is favored over interior ion hydration which is destabilized by noncooperative effects. The potential of the ABN + -H 2 O dimer is characterized in detail and supports the cluster growth derived from the IRPD spectra. Although the N–H bonds are destabilized by stepwise microhydration, which is accompanied by increasing charge transfer from ABN + to the solvent cluster, no proton transfer to the solvent is observed for n ≤ 4.

Description: We attempt to simulate the heterogeneous nucleation of ice at model silver-iodide surfaces and find relatively facile ice nucleation and growth at the Ag + terminated basal face, but never see nucleation at the I − terminated basal face or the prism and normal faces. Water molecules strongly adsorb onto the Ag + terminated face to give a well-ordered hexagonal ice-like bilayer that then acts as a template for further ice growth.

Description: The level of hydration controls the cohesion between apposed lamellae of saturated free fatty acids found in the lipid matrix of stratum corneum, the outermost layer of mammalian skin. This multilamellar lipid matrix is highly impermeable to water and ions, so that the local hydration shell of its fatty acids may not always be in equilibrium with the acidity and relative humidity, which significantly change over a course of days during skin growth. The homeostasis of the stratum corneum at each moment of its growth likely requires a balance between two factors, which affect in opposite ways the diffusion of hydrophilic species through the stratum corneum: (i) an increase in water order as the lipid lamellae come in closer contact, and (ii) a decrease in water order as the fraction of charged fatty acids is lowered by pH. Herein molecular dynamics simulations are employed to estimate the impact of both effects on water molecules confined between lamellae of fatty acids. Under conditions where membrane undulations are energetically favorable, the charged fatty acids are able to sequester cations around points of contact between lamellae that are fully dehydrated, while essentially maintaining a multilamellar structure for the entire system. This observation suggests that the undulations of the fatty acid lamellae control the diffusion of hydrophilic species through the water phase by altering the positional and rotational order of water molecules in the embedded/occluded “droplets.”

Description: Protein collapse during folding is often assumed to be driven by a hydrophobic solvation energy (Δ G vdw ) that scales linearly with solvent-accessible surface area ( A ). In a previous study, we argued that Δ G vdw , as well as its attractive (Δ G att ) and repulsive (Δ G rep ) components, was not simply a linear function of A . We found that the surface tensions, γ rep , γ att , and γ vdw , gotten from Δ G rep , Δ G att , and Δ G vdw against A for four configurations of deca-alanine differed from those obtained for a set of alkanes. In the present study, we extend our analysis to fifty decaglycine structures and atomic decompositions. We find that different configurations of decaglycine generate different estimates of γ rep . Additionally, we considered the reconstruction of the solvation free energy from scaling the free energy of solvation of each atom type, free in solution. The free energy of the isolated atoms, scaled by the inverse surface area the atom would expose in the molecule does not reproduce the γ rep for the intact decaglycines. Finally, γ att for the decaglycine conformations is much larger in magnitude than those for deca-alanine or the alkanes, leading to large negative values of γ vdw (−74 and −56 cal/mol/Å 2 for CHARMM27 and AMBER ff12sb force fields, respectively). These findings imply that Δ G vdw favors extended rather than compact structures for decaglycine. We find that Δ G rep and Δ G vdw have complicated dependencies on multibody correlations between solute atoms, on the geometry of the molecular surface, and on the chemical identities of the atoms.

Description: The nucleation and growth of Pt nanoparticles (NP’s) on rutile TiO 2 (110) surfaces with O on-top atoms (oxidized TiO 2 ), surface O vacancies, and H adatoms, respectively (reduced TiO 2 ), was studied by means of scanning tunneling microscopy (STM) experiments and density functional theory calculations. At room temperature, Pt was found to be trapped at O on-top atoms and surface O vacancies, leading to rather small Pt NP’s. In contrast, on surfaces with H adatoms the mobility of Pt was much larger. As a result, large Pt NP's were found at room temperature on TiO 2 (110) surfaces with H adatoms. However, at ∼150 K the diffusion of Pt was kinetically hindered on all TiO 2 (110) surfaces considered. STM data acquired after vacuum-annealing at 800 K showed comparable results on all TiO 2 (110) surfaces because the diffusion of Pt is not influenced by surface defects at such high temperatures.

Description: Based on the exact factorization of the electron-nuclear wave function, we have recently proposed a mixed quantum-classical scheme [A. Abedi, F. Agostini, and E. K. U. Gross, Europhys. Lett.106, 33001 (2014)] to deal with non-adiabatic processes. Here we present a comprehensive description of the formalism, including the full derivation of the equations of motion. Numerical results are presented for a model system for non-adiabatic charge transfer in order to test the performance of the method and to validate the underlying approximations.